Zinc in PDB 5wfc: Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK343

The structure of Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK343, PDB code: 5wfc was solved by M.A.Bratkowski, X.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.72 / 2.28
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	117.587, 137.794, 222.332, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 20.3

The binding sites of Zinc atom in the Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK343 (pdb code 5wfc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK343, PDB code: 5wfc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK343


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK343 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8001 b:28.8 occ:1.00 SG B:CYS727 2.3 30.4 1.0 SG B:CYS755 2.4 27.6 1.0 SG B:CYS748 2.4 28.6 1.0 SG B:CYS760 2.4 28.8 1.0 CB B:CYS727 3.1 31.1 1.0 CB B:CYS755 3.1 26.8 1.0 CB B:CYS760 3.3 29.3 1.0 CB B:CYS748 3.4 28.0 1.0 N B:CYS727 3.5 34.3 1.0 CA B:CYS755 3.5 26.3 1.0 ZN B:ZN8003 3.8 30.3 1.0 ZN B:ZN8002 3.8 28.4 1.0 CA B:CYS727 3.9 31.8 1.0 O B:HOH8198 4.3 27.5 1.0 SG B:CYS746 4.3 29.6 1.0 N B:CYS755 4.5 25.6 1.0 N B:ASP756 4.6 26.6 1.0 CA B:CYS760 4.6 32.5 1.0 C B:GLY726 4.6 35.2 1.0 C B:CYS755 4.6 25.9 1.0 SG B:CYS736 4.7 29.5 1.0 SG B:CYS763 4.7 29.4 1.0 CA B:CYS748 4.7 30.6 1.0 C B:CYS727 4.8 37.6 1.0 N B:CYS748 4.9 29.5 1.0 CA B:GLY726 4.9 34.8 1.0 O B:CYS727 5.0 36.7 1.0

Zinc binding site 2 out of 8 in the Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK343


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK343 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8002 b:28.4 occ:1.00 SG B:CYS736 2.3 29.5 1.0 SG B:CYS755 2.3 27.6 1.0 SG B:CYS763 2.4 29.4 1.0 SG B:CYS784 2.4 27.0 1.0 CB B:CYS784 3.2 27.6 1.0 CB B:CYS736 3.3 28.7 1.0 CB B:CYS755 3.3 26.8 1.0 CB B:CYS763 3.3 30.4 1.0 ZN B:ZN8003 3.8 30.3 1.0 ZN B:ZN8001 3.8 28.8 1.0 SG B:CYS727 3.9 30.4 1.0 CA B:CYS784 4.0 28.0 1.0 CB B:ALA765 4.4 27.2 1.0 CB B:CYS760 4.6 29.3 1.0 CB B:ASN786 4.7 26.1 1.0 CA B:CYS736 4.7 29.4 1.0 CA B:CYS755 4.7 26.3 1.0 CA B:CYS763 4.7 32.4 1.0 C B:CYS784 5.0 31.2 1.0 N B:CYS784 5.0 28.7 1.0

Zinc binding site 3 out of 8 in the Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK343


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK343 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8003 b:30.3 occ:1.00 SG B:CYS746 2.3 29.6 1.0 SG B:CYS727 2.3 30.4 1.0 SG B:CYS729 2.4 32.1 1.0 SG B:CYS736 2.4 29.5 1.0 CB B:CYS727 3.1 31.1 1.0 CB B:CYS746 3.2 30.5 1.0 CB B:CYS736 3.3 28.7 1.0 CB B:CYS729 3.4 32.6 1.0 CA B:CYS736 3.7 29.4 1.0 ZN B:ZN8002 3.8 28.4 1.0 ZN B:ZN8001 3.8 28.8 1.0 SG B:CYS755 4.0 27.6 1.0 CA B:CYS746 4.0 31.5 1.0 N B:CYS729 4.2 33.5 1.0 N B:CYS736 4.3 30.2 1.0 CA B:CYS729 4.5 33.6 1.0 CA B:CYS727 4.5 31.8 1.0 C B:CYS746 4.8 31.2 1.0 C B:CYS727 4.9 37.6 1.0 SG B:CYS763 4.9 29.4 1.0 CB B:CYS748 4.9 28.0 1.0 N B:ALA728 4.9 33.5 1.0 CB B:CYS763 5.0 30.4 1.0

Zinc binding site 4 out of 8 in the Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK343


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK343 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8004 b:37.4 occ:1.00 NE2 B:HIS687 2.0 41.3 1.0 SG B:CYS691 2.2 40.3 1.0 SG B:CYS697 2.3 42.4 1.0 SG B:CYS685 2.4 39.2 1.0 CD2 B:HIS687 2.9 38.7 1.0 CB B:CYS691 3.0 38.4 1.0 CE1 B:HIS687 3.0 40.5 1.0 CB B:CYS685 3.1 34.1 1.0 CB B:CYS697 3.2 37.9 1.0 CA B:CYS691 3.6 37.1 1.0 ZN B:ZN8006 3.7 33.1 1.0 ZN B:ZN8005 3.9 36.4 1.0 SG B:CYS709 3.9 32.4 1.0 CA B:CYS697 4.1 40.2 1.0 CG B:HIS687 4.1 40.3 1.0 ND1 B:HIS687 4.1 40.7 1.0 CA B:CYS685 4.5 37.5 1.0 O B:HOH8333 4.6 47.6 1.0 N B:CYS691 4.6 37.6 1.0 C B:CYS691 4.8 40.7 1.0 SG B:CYS699 4.8 34.8 1.0 C B:CYS697 4.9 42.0 1.0 CB B:CYS699 4.9 34.9 1.0 SG B:CYS715 5.0 37.2 1.0 C B:CYS685 5.0 43.3 1.0

Zinc binding site 5 out of 8 in the Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK343


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK343 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8005 b:36.4 occ:1.00 SG B:CYS720 2.2 36.0 1.0 SG B:CYS709 2.3 32.4 1.0 SG B:CYS715 2.3 37.2 1.0 SG B:CYS691 2.6 40.3 1.0 CB B:CYS720 3.2 41.6 1.0 CB B:CYS709 3.2 33.3 1.0 CB B:CYS691 3.3 38.4 1.0 CB B:CYS715 3.3 34.8 1.0 ZN B:ZN8004 3.9 37.4 1.0 ZN B:ZN8006 3.9 33.1 1.0 SG B:CYS685 4.2 39.2 1.0 O B:HOH8177 4.2 46.7 1.0 CA B:CYS720 4.7 45.5 1.0 CB B:LEU722 4.7 39.2 1.0 CA B:CYS709 4.7 36.6 1.0 CA B:CYS715 4.7 38.8 1.0 CA B:CYS691 4.7 37.1 1.0 N B:LYS723 5.0 38.8 1.0 CB B:CYS713 5.0 30.5 1.0

Zinc binding site 6 out of 8 in the Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK343


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK343 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8006 b:33.1 occ:1.00 SG B:CYS709 2.2 32.4 1.0 SG B:CYS699 2.3 34.8 1.0 SG B:CYS685 2.4 39.2 1.0 SG B:CYS713 2.4 31.4 1.0 CB B:CYS709 3.1 33.3 1.0 CB B:CYS699 3.2 34.9 1.0 CB B:CYS713 3.3 30.5 1.0 CB B:CYS685 3.4 34.1 1.0 CA B:CYS709 3.6 36.6 1.0 ZN B:ZN8004 3.7 37.4 1.0 ZN B:ZN8005 3.9 36.4 1.0 N B:CYS685 4.0 32.2 1.0 O B:HOH8231 4.0 35.8 1.0 SG B:CYS697 4.1 42.4 1.0 CA B:CYS685 4.3 37.5 1.0 SG B:CYS715 4.5 37.2 1.0 N B:CYS709 4.6 31.1 1.0 CA B:CYS699 4.6 35.9 1.0 SG B:CYS691 4.6 40.3 1.0 C B:CYS709 4.7 36.5 1.0 CA B:CYS713 4.7 38.7 1.0 N B:GLU710 4.7 35.5 1.0 N B:CYS699 4.8 33.7 1.0

Zinc binding site 7 out of 8 in the Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK343


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK343 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8007 b:23.9 occ:1.00 ND1 B:HIS518 2.1 26.8 1.0 SG B:CYS511 2.4 20.0 1.0 SG B:CYS508 2.4 23.2 1.0 SG B:CYS516 2.4 20.4 1.0 CE1 B:HIS518 3.0 28.8 1.0 CB B:CYS508 3.0 21.3 1.0 CG B:HIS518 3.0 30.2 1.0 CB B:CYS516 3.2 18.8 1.0 CB B:CYS511 3.4 20.7 1.0 CB B:HIS518 3.4 24.2 1.0 O B:HOH8394 3.8 28.6 1.0 N B:CYS511 3.9 21.4 1.0 N B:HIS518 4.0 21.9 1.0 NE2 B:HIS518 4.1 29.8 1.0 CD2 B:HIS518 4.1 28.3 1.0 CA B:CYS511 4.1 22.3 1.0 CA B:HIS518 4.4 25.3 1.0 O B:HOH8388 4.4 28.4 1.0 N B:GLU517 4.5 22.9 1.0 CA B:CYS508 4.5 25.5 1.0 CA B:CYS516 4.6 20.9 1.0 C B:CYS511 4.7 24.4 1.0 N B:PHE512 4.8 21.7 1.0 C B:CYS516 4.8 21.1 1.0 CB B:ILE510 4.8 24.8 1.0 O B:SER513 4.8 26.1 1.0 N B:SER513 5.0 24.1 1.0 C B:ILE510 5.0 27.9 1.0

Zinc binding site 8 out of 8 in the Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK343


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Humanized Mutant of the Chaetomium Thermophilum Polycomb Repressive Complex 2 Bound to the Inhibitor GSK343 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn8008 b:55.1 occ:1.00 SG B:CYS570 2.3 55.3 1.0 SG B:CYS625 2.3 56.5 1.0 SG B:CYS615 2.4 68.4 1.0 SG B:CYS574 2.5 68.8 1.0 CB B:CYS625 2.9 57.0 1.0 CB B:CYS574 3.3 65.3 1.0 CA B:CYS574 3.4 61.0 1.0 CB B:CYS615 3.4 54.6 1.0 CB B:CYS570 3.6 57.9 1.0 CA B:CYS615 3.6 48.3 1.0 N B:TYR575 3.8 61.2 1.0 N B:CYS615 4.0 48.9 1.0 CD1 B:TYR575 4.1 81.2 1.0 C B:CYS574 4.1 60.0 1.0 N B:CYS570 4.2 72.5 1.0 CA B:CYS625 4.4 57.3 1.0 CA B:CYS570 4.5 69.0 1.0 N B:CYS574 4.5 60.6 1.0 C B:GLU614 4.7 54.2 1.0 CE1 B:TYR575 4.8 83.1 1.0 CB B:GLU614 4.9 64.8 1.0 O B:CYS570 4.9 68.8 1.0 C B:CYS615 5.0 48.4 1.0

M.Bratkowski, X.Yang, X.Liu. An Evolutionarily Conserved Structural Platform For PRC2 Inhibition By A Class of EZH2 Inhibitors. Sci Rep V. 8 9092 2018.
ISSN: ESSN 2045-2322
PubMed: 29904056
DOI: 10.1038/S41598-018-27175-W